This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. The goal of this project is to develop a novel algorithm for remote protein sequence homology detection. Our approach involves developing a more accurate profile-profile alignment algorithm for detecting Pfam (http://www.sanger.ac.uk/Software/Pfam/) domains in a query protein of interest. We propose to use the TeraGrid to generate protein sequence profiles on 200,000 representative sequences from the Pfam-A and Pfam-B families using a modified PSI-BLAST algorithm.